Simion ion trajectory simulations

SIMION software

Annemieke Petrignani purchased a license for Simion 8 through Leiden University, for use on the FELICE FTICR instrument. The installer files are located at

\\felixdisk.science.ru.nl\hfmlfelix\general\Software\Simion81

SIMION short instructions

• Create a geometry file. A sample is here
• Turn it into a potential array
  • create new PA --> Use Geometry File
  • save the new PA as xxx.pa# (this indicates it is a multi-electrode potential array)
  • refine the PA (this will solve the Poisson equations over the whole volume of the potential array for each electrode n, and will creates multiple files xxx.pa'''<n> )
• once done, load one of your potential arrays (the xxx.pa0 file)
• View/Load workbench

This will open a new window in Simion, where trajectory simulations can be done, multiple arrays can be included, and positioned with respect to each other

Defining ion packages

• Done through the Particle-->Define partticle button on the workbench
• Better: define them using an external xxx.fly2 file. A sample is here

Controlling changing potentials during the simulation

• Done through a xxx.lua control file with the same name as the xxx.iob workbench file. A sample is here, which calls another file here

Evaluating results

• Simion can write tons of data to an output file, such as the time of 'death' of an ion, when it hits an electrode.
• Typically, you can either define a target electrode to purposefully hit an ion with (a detector electrode)
• Alternatively, you can evaluate where the ions are after a fixed time period

Automating runs and evaluation

• Simion can be run interactively, but also non-interactively, even without GUI, from the command line.
• I (joost) chose to control it using a Python script (can't upload yet, stupid wiki), but any software that can make system calls (e.g. Matlab) should do.
• Leo Meerts implemented a WINE-called implementation on his Linux machine rs58 and controls it from the GA genetic algorithm software

Free-electron laser for Intra-Cavity Experiments

Python - a programming language that lets you work quickly and integrate systems more effectively.